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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtgtatgatgttaatgaaaattgttcggtgaaaattgtgcatttggaaaacctaggttttgtggtttctgatctgtattgggtgttggttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGATTCCAAGGAAAAGAACAGGAAATTTGTGGAGACCATTGAACTCCAAATT

Basic information

species Glycine max
transcript GLYMA12G31040.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31040.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------actgtgtatgatgttaatgaaaattgttcggtgaaaattgtgcatttggaaaacctaggttttgtggtttctgatctgtattgggtgttggttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGATTCCAAGGAAAAGAACAGGAAATTTGTGGAGACCATTGAACTCCAAATT
                                                                        |   |    ||||  |||||||| |       ||  ||| ||   |         |||| |     ||||    |  |   | ||   |  | ||||||||| ||||||||||||||||||||||| ||| ||   ||  | | ||| |||||||| || ||  | || |||   ||||||||||| |||||||| 
gttcatccttattttattgtggctcaggaactttgttgatgcagaagttctaaaatgattacatttttttaattcttatctttaactaaaattgtccttgatttatgttgctttgaaattgaactttttttctatcccctgactcattatctttctttcat-ctacagTAAGCTCCAGAGTGATGCTCTTAGAGAAGCCATCACAAACATTGTTAATGAATCCAAGGAGAAAAAGCGTAATTTTACTGAGACCATTGAGCTCCAAATC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|151413165|gb|EV282973.1|EV282973
EST:     CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAG                         TAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
genomic: CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAGgtattcattc ... gttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
EST: gi|7232575|gb|AW567930.1|AW567930
EST:     CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAG                         TAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
genomic: CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAGgtattcattc ... gttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
EST: gi|208099220|gb|GD898749.1|GD898749
EST:     CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAG                         TAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
genomic: CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAGgtattcattc ... gttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
EST: gi|208276001|gb|GE074295.1|GE074295
EST:     CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAG                         TAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
genomic: CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAGgtattcattc ... gttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
EST: gi|19934524|gb|BQ079554.1|BQ079554
EST:     CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAG                         TAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
genomic: CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAGgtattcattc ... gttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
EST: gi|298169144|gb|HO020504.1|HO020504
EST:     CTGTACCCGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAG                         TAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
genomic: CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAGgtattcattc ... gttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
EST: gi|192315372|gb|FK009636.1|FK009636
EST:     CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAG                         TAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA
genomic: CTGTACCTGCCTAGCCATTGATTTGGAAAAGTCCAAGCTTCAAAGATGAGgtattcattc ... gttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaaaacctaggttttgtggtttctgatctgtattgggtgttggttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGATTCCAAGGAAAAGAACAGGAAATTTGTGGAGACCATTGAACTCCAAATT
                       ttctgat  putative branch site (score: 3)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgtgtatgatgttaatgaaaattgttcggtgaaaattgtgcatttggaaaacctaggttttgtggtttctgatctgtattgggtgttggttgttgcagTAAGCTTCAGAGTGATGCTCTTAGAGAAGCTATCTCAGGAATCATGACTGATTCCAAGGAAAAGAACAGGAAATTTGTGGAGACCATTGAACTCCAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA